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<div class="section" id="descriptors-for-atomic-environments">
<h1>Descriptors for atomic environments<a class="headerlink" href="#descriptors-for-atomic-environments" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="quippy.descriptors.Descriptor">
<em class="property">class </em><code class="descclassname">quippy.descriptors.</code><code class="descname">Descriptor</code><span class="sig-paren">(</span><em>args_str</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/quippy/descriptors.html#Descriptor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#quippy.descriptors.Descriptor" title="Permalink to this definition">¶</a></dt>
<dd><p>Pythonic wrapper for GAP descriptor module</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>args_str</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input string(len=-1)</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">__init__initialise</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.
Class is wrapper around Fortran type <code class="docutils literal notranslate"><span class="pre">descriptor</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
<p class="rubric">Methods</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="#quippy.descriptors.Descriptor.calc_descriptor" title="quippy.descriptors.Descriptor.calc_descriptor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">calc_descriptor</span></code></a>(at,&nbsp;*args,&nbsp;**kw)</td>
<td>Calculates all descriptors of this type in the Atoms object, and returns the array of descriptor values.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#quippy.descriptors.Descriptor.count" title="quippy.descriptors.Descriptor.count"><code class="xref py py-obj docutils literal notranslate"><span class="pre">count</span></code></a>(at,&nbsp;*args,&nbsp;**kw)</td>
<td>Returns how many descriptors of this type are found in the Atoms object.</td>
</tr>
</tbody>
</table>
<dl class="method">
<dt id="quippy.descriptors.Descriptor.calc">
<code class="descname">calc</code><span class="sig-paren">(</span><em>at</em>, <em>*args</em>, <em>**kw</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/quippy/descriptors.html#Descriptor.calc"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#quippy.descriptors.Descriptor.calc" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates all descriptors of this type in the Atoms object, and
gradients if grad=True. Results can be accessed dictionary- or
attribute-style; ‘descriptor’ contains descriptor values, 
‘descriptor_index_0based’ contains the 0-based indices of the central 
atom(s) in each descriptor, ‘grad’ contains gradients, 
‘grad_index_0based’ contains indices to gradients (descriptor, atom).
Cutoffs and gradients of cutoffs are also returned.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Descriptor.calc_array">
<code class="descname">calc_array</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>out</em>, <em>covariance_cutoff</em>, <em>index</em>, <em>grad_out</em>, <em>grad_index</em>, <em>grad_pos</em>, <em>grad_covariance_cutoff</em>, <em>args_str</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Descriptor.calc_array" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><code class="xref py py-class docutils literal notranslate"><span class="pre">atoms</span></code> object</span></dt>
<dd></dd>
<dt><strong>descriptor_out</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-2 array(‘d’) with bounds (qp_n0,qp_n1), optional</span></dt>
<dd></dd>
<dt><strong>covariance_cutoff</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-1 array(‘d’) with bounds (qp_n2), optional</span></dt>
<dd></dd>
<dt><strong>descriptor_index</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-2 array(‘i’) with bounds (qp_n3,qp_n4), optional</span></dt>
<dd></dd>
<dt><strong>grad_descriptor_out</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-3 array(‘d’) with bounds (qp_n5,qp_n6,qp_n7), optional</span></dt>
<dd></dd>
<dt><strong>grad_descriptor_index</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-2 array(‘i’) with bounds (qp_n8,qp_n9), optional</span></dt>
<dd></dd>
<dt><strong>grad_descriptor_pos</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-2 array(‘d’) with bounds (qp_n10,qp_n11), optional</span></dt>
<dd></dd>
<dt><strong>grad_covariance_cutoff</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-2 array(‘d’) with bounds (qp_n12,qp_n13), optional</span></dt>
<dd></dd>
<dt><strong>args_str</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input string(len=-1), optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">descriptor_calc_array</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Descriptor.calc_descriptor">
<code class="descname">calc_descriptor</code><span class="sig-paren">(</span><em>at</em>, <em>*args</em>, <em>**kw</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/quippy/descriptors.html#Descriptor.calc_descriptor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#quippy.descriptors.Descriptor.calc_descriptor" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates all descriptors of this type in the Atoms object, and
returns the array of descriptor values. Does not compute gradients; use
calc(at, grad=True, …) for that.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Descriptor.count">
<code class="descname">count</code><span class="sig-paren">(</span><em>at</em>, <em>*args</em>, <em>**kw</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/quippy/descriptors.html#Descriptor.count"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#quippy.descriptors.Descriptor.count" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns how many descriptors of this type are found in the Atoms
object.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Descriptor.cutoff">
<code class="descname">cutoff</code><span class="sig-paren">(</span><span class="optional">[</span><em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Descriptor.cutoff" title="Permalink to this definition">¶</a></dt>
<dd><p>descriptor_cutoff([error])</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first docutils">
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>ret_descriptor_cutoff</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">cutoff</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Descriptor.descriptor_sizes">
<code class="descname">descriptor_sizes</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>mask</em>, <em>n_index</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Descriptor.descriptor_sizes" title="Permalink to this definition">¶</a></dt>
<dd><p>descriptor_descriptor_sizes(at,[mask,n_index,error])</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><code class="xref py py-class docutils literal notranslate"><span class="pre">atoms</span></code> object</span></dt>
<dd></dd>
<dt><strong>n_descriptors</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>n_cross</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>mask</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input rank-1 array(‘i’) with bounds (qp_n0), optional</span></dt>
<dd></dd>
<dt><strong>n_index</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">sizes</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Descriptor.dimensions">
<code class="descname">dimensions</code><span class="sig-paren">(</span><span class="optional">[</span><em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Descriptor.dimensions" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>ret_descriptor_dimensions</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">descriptor_dimensions</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Descriptor.mpi_setup">
<code class="descname">mpi_setup</code><span class="sig-paren">(</span><em>at</em>, <em>mpi</em>, <em>n0</em><span class="optional">[</span>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Descriptor.mpi_setup" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><code class="xref py py-class docutils literal notranslate"><span class="pre">atoms</span></code> object</span></dt>
<dd></dd>
<dt><strong>mpi</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="mpi_context.html#quippy.mpi_context.MPI_context" title="quippy.mpi_context.MPI_context"><code class="xref py py-class docutils literal notranslate"><span class="pre">MPI_context</span></code></a> object</span></dt>
<dd></dd>
<dt><strong>n0</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input int</span></dt>
<dd><p class="first last">shape(qp_mpi_mask,0)</p>
</dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>mpi_mask</strong> <span class="classifier-delimiter">:</span> <span class="classifier">rank-1 array(‘i’) with bounds (qp_n0)</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">descriptor_mpi_setup</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Descriptor.n_permutations">
<code class="descname">n_permutations</code><span class="sig-paren">(</span><span class="optional">[</span><em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Descriptor.n_permutations" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>ret_descriptor_n_permutations</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">descriptor_n_permutations</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Descriptor.permutations">
<code class="descname">permutations</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/quippy/descriptors.html#Descriptor.permutations"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#quippy.descriptors.Descriptor.permutations" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns array containing all valid permutations of this descriptor.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Descriptor.sizes">
<code class="descname">sizes</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>mask</em>, <em>n_index</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Descriptor.sizes" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><code class="xref py py-class docutils literal notranslate"><span class="pre">atoms</span></code> object</span></dt>
<dd></dd>
<dt><strong>n_descriptors</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>n_cross</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>mask</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input rank-1 array(‘i’) with bounds (qp_n0), optional</span></dt>
<dd></dd>
<dt><strong>n_index</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">descriptor_sizes</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.descriptors.Descriptor.n_dim">
<code class="descname">n_dim</code><a class="headerlink" href="#quippy.descriptors.Descriptor.n_dim" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of dimensions</p>
</dd></dl>

<dl class="attribute">
<dt id="quippy.descriptors.Descriptor.n_perm">
<code class="descname">n_perm</code><a class="headerlink" href="#quippy.descriptors.Descriptor.n_perm" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of permutations</p>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="quippy.descriptors.Soap">
<em class="property">class </em><code class="descclassname">quippy.descriptors.</code><code class="descname">Soap</code><span class="sig-paren">(</span><em>args_str</em><span class="optional">[</span>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Soap" title="Permalink to this definition">¶</a></dt>
<dd><p class="rubric">args_str options</p>
<table border="1" class="docutils">
<colgroup>
<col width="33%" />
<col width="6%" />
<col width="17%" />
<col width="45%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Name</th>
<th class="head">Type</th>
<th class="head">Default</th>
<th class="head">Comments</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>Z</td>
<td>None</td>
<td>//MANDATORY//</td>
<td>Atomic numbers to be considered for
central atom, must be a list</td>
</tr>
<tr class="row-odd"><td>atom_sigma</td>
<td>None</td>
<td>PARAM_MANDATORY</td>
<td>Width of atomic Gaussians for soap-type
descriptors</td>
</tr>
<tr class="row-even"><td>average</td>
<td>None</td>
<td>False</td>
<td>Whether to calculate averaged SOAP -
one descriptor per atoms object. If
false (default) atomic SOAP is
returned.</td>
</tr>
<tr class="row-odd"><td>basis_error_exponent</td>
<td>float</td>
<td>10.0</td>
<td>10^(-basis_error_exponent) is the max
difference between the target and the
expanded function</td>
</tr>
<tr class="row-even"><td>central_reference_all_species</td>
<td>None</td>
<td>False</td>
<td>Place a Gaussian reference for all atom
species densities.”// “By default (F)
only consider when neighbour is the
same species as centre</td>
</tr>
<tr class="row-odd"><td>central_weight</td>
<td>None</td>
<td>1.0</td>
<td>Weight of central atom in environment</td>
</tr>
<tr class="row-even"><td>covariance_sigma0</td>
<td>None</td>
<td>0.0</td>
<td>Sigma_0 parameter in polynomial
covariance function</td>
</tr>
<tr class="row-odd"><td>cutoff</td>
<td>None</td>
<td>PARAM_MANDATORY</td>
<td>Cutoff for soap-type descriptors</td>
</tr>
<tr class="row-even"><td>cutoff_dexp</td>
<td>None</td>
<td>0</td>
<td>Cutoff decay exponent</td>
</tr>
<tr class="row-odd"><td>cutoff_rate</td>
<td>None</td>
<td>1.0</td>
<td>Inverse cutoff decay rate</td>
</tr>
<tr class="row-even"><td>cutoff_scale</td>
<td>None</td>
<td>1.0</td>
<td>Cutoff decay scale</td>
</tr>
<tr class="row-odd"><td>cutoff_transition_width</td>
<td>None</td>
<td>0.50</td>
<td>Cutoff transition width for soap-type
descriptors</td>
</tr>
<tr class="row-even"><td>diagonal_radial</td>
<td>None</td>
<td>False</td>
<td>Only return the n1=n2 elements of the
power spectrum.</td>
</tr>
<tr class="row-odd"><td>l_max</td>
<td>None</td>
<td>PARAM_MANDATORY</td>
<td>L_max (spherical harmonics basis band
limit) for soap-type descriptors</td>
</tr>
<tr class="row-even"><td>n_Z</td>
<td>None</td>
<td>1</td>
<td>How many different types of central
atoms to consider</td>
</tr>
<tr class="row-odd"><td>n_max</td>
<td>None</td>
<td>PARAM_MANDATORY</td>
<td>N_max (number of radial basis
functions) for soap-type descriptors</td>
</tr>
<tr class="row-even"><td>n_species</td>
<td>None</td>
<td>1</td>
<td>Number of species for the descriptor</td>
</tr>
<tr class="row-odd"><td>normalise</td>
<td>None</td>
<td>True</td>
<td>Normalise descriptor so magnitude is 1.
In this case the kernel of two
equivalent environments is 1.</td>
</tr>
<tr class="row-even"><td>species_Z</td>
<td>None</td>
<td>//MANDATORY//</td>
<td>Atomic number of species</td>
</tr>
<tr class="row-odd"><td>xml_version</td>
<td>int</td>
<td>1426512068</td>
<td>Version of GAP the XML potential file
was created</td>
</tr>
</tbody>
</table>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>args_str</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input string(len=-1)</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">__init__initialise</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.
Class is wrapper around Fortran type <code class="docutils literal notranslate"><span class="pre">soap</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
<p class="rubric">Methods</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="#quippy.descriptors.Soap.cutoff_" title="quippy.descriptors.Soap.cutoff_"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cutoff_</span></code></a>([error])</td>
<td>soap_cutoff([error])</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#quippy.descriptors.Soap.descriptor_sizes" title="quippy.descriptors.Soap.descriptor_sizes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">descriptor_sizes</span></code></a>(at,[mask,n_index,error])</td>
<td>soap_descriptor_sizes(at,[mask,n_index,error])</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#quippy.descriptors.Soap.sizes" title="quippy.descriptors.Soap.sizes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sizes</span></code></a>(at,[mask,n_index,error])</td>
<td><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"></td>
</tr>
</tbody>
</table>
</td>
</tr>
</tbody>
</table>
<dl class="method">
<dt id="quippy.descriptors.Soap.cutoff_">
<code class="descname">cutoff_</code><span class="sig-paren">(</span><span class="optional">[</span><em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Soap.cutoff_" title="Permalink to this definition">¶</a></dt>
<dd><p>soap_cutoff([error])</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first docutils">
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>ret_soap_cutoff</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">cutoff</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Soap.descriptor_sizes">
<code class="descname">descriptor_sizes</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>mask</em>, <em>n_index</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Soap.descriptor_sizes" title="Permalink to this definition">¶</a></dt>
<dd><p>soap_descriptor_sizes(at,[mask,n_index,error])</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><code class="xref py py-class docutils literal notranslate"><span class="pre">atoms</span></code> object</span></dt>
<dd></dd>
<dt><strong>n_descriptors</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>n_cross</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>mask</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input rank-1 array(‘i’) with bounds (qp_n0), optional</span></dt>
<dd></dd>
<dt><strong>n_index</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">sizes</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.Soap.sizes">
<code class="descname">sizes</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>mask</em>, <em>n_index</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.Soap.sizes" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><code class="xref py py-class docutils literal notranslate"><span class="pre">atoms</span></code> object</span></dt>
<dd></dd>
<dt><strong>n_descriptors</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>n_cross</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>mask</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input rank-1 array(‘i’) with bounds (qp_n0), optional</span></dt>
<dd></dd>
<dt><strong>n_index</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">soap_sizes</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

</dd></dl>

<dl class="class">
<dt id="quippy.descriptors.General_monomer">
<em class="property">class </em><code class="descclassname">quippy.descriptors.</code><code class="descname">General_monomer</code><span class="sig-paren">(</span><em>args_str</em><span class="optional">[</span>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.General_monomer" title="Permalink to this definition">¶</a></dt>
<dd><p class="rubric">args_str options</p>
<table border="1" class="docutils">
<colgroup>
<col width="20%" />
<col width="5%" />
<col width="20%" />
<col width="54%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Name</th>
<th class="head">Type</th>
<th class="head">Default</th>
<th class="head">Comments</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>atom_ordercheck</td>
<td>None</td>
<td>true</td>
<td>T: find molecules. F: go by order of
atoms</td>
</tr>
<tr class="row-odd"><td>cutoff</td>
<td>None</td>
<td>0.00</td>
<td>Cutoff for general_monomer-type
descriptors</td>
</tr>
<tr class="row-even"><td>power</td>
<td>None</td>
<td>1.0</td>
<td>Power of distances to be used in the
kernel</td>
</tr>
<tr class="row-odd"><td>signature</td>
<td>str</td>
<td>PARAM_MANDATORY</td>
<td>Atomic numbers of monomer one, format
{Z1 Z2 Z3 …}</td>
</tr>
<tr class="row-even"><td>strict</td>
<td>None</td>
<td>true</td>
<td>Raise error if not all atoms assigned
to monomer</td>
</tr>
</tbody>
</table>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>args_str</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input string(len=-1)</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">__init__initialise</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.
Class is wrapper around Fortran type <code class="docutils literal notranslate"><span class="pre">general_monomer</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
<p class="rubric">Methods</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="#quippy.descriptors.General_monomer.cutoff_" title="quippy.descriptors.General_monomer.cutoff_"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cutoff_</span></code></a>([error])</td>
<td>general_monomer_cutoff([error])</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#quippy.descriptors.General_monomer.descriptor_sizes" title="quippy.descriptors.General_monomer.descriptor_sizes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">descriptor_sizes</span></code></a>(at,[mask,n_index,error])</td>
<td>general_monomer_descriptor_sizes(at,[mask,n_index,error])</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#quippy.descriptors.General_monomer.sizes" title="quippy.descriptors.General_monomer.sizes"><code class="xref py py-obj docutils literal notranslate"><span class="pre">sizes</span></code></a>(at,[mask,n_index,error])</td>
<td><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"></td>
</tr>
</tbody>
</table>
</td>
</tr>
</tbody>
</table>
<dl class="method">
<dt id="quippy.descriptors.General_monomer.cutoff_">
<code class="descname">cutoff_</code><span class="sig-paren">(</span><span class="optional">[</span><em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.General_monomer.cutoff_" title="Permalink to this definition">¶</a></dt>
<dd><p>general_monomer_cutoff([error])</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first docutils">
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>ret_general_monomer_cutoff</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">cutoff</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.General_monomer.descriptor_sizes">
<code class="descname">descriptor_sizes</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>mask</em>, <em>n_index</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.General_monomer.descriptor_sizes" title="Permalink to this definition">¶</a></dt>
<dd><p>general_monomer_descriptor_sizes(at,[mask,n_index,error])</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><code class="xref py py-class docutils literal notranslate"><span class="pre">atoms</span></code> object</span></dt>
<dd></dd>
<dt><strong>n_descriptors</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>n_cross</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>mask</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input rank-1 array(‘i’) with bounds (qp_n0), optional</span></dt>
<dd></dd>
<dt><strong>n_index</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">sizes</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

<dl class="method">
<dt id="quippy.descriptors.General_monomer.sizes">
<code class="descname">sizes</code><span class="sig-paren">(</span><em>at</em><span class="optional">[</span>, <em>mask</em>, <em>n_index</em>, <em>error</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#quippy.descriptors.General_monomer.sizes" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>at</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><code class="xref py py-class docutils literal notranslate"><span class="pre">atoms</span></code> object</span></dt>
<dd></dd>
<dt><strong>n_descriptors</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>n_cross</strong> <span class="classifier-delimiter">:</span> <span class="classifier">int</span></dt>
<dd></dd>
<dt><strong>mask</strong> <span class="classifier-delimiter">:</span> <span class="classifier">input rank-1 array(‘i’) with bounds (qp_n0), optional</span></dt>
<dd></dd>
<dt><strong>n_index</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
<dt><strong>error</strong> <span class="classifier-delimiter">:</span> <span class="classifier">in/output rank-0 array(int,’i’), optional</span></dt>
<dd></dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">References</p>
<p>Routine is wrapper around Fortran routine <code class="docutils literal notranslate"><span class="pre">general_monomer_sizes</span></code> defined in file <a class="reference external" href="https://github.com/libAtoms/QUIP/blob/public/src/GAP/descriptors.f95">src/GAP/descriptors.f95</a>.</p>
</dd></dl>

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